<Fewer/Less> than one percent of Spanish students around the world ...

I know that you use few for count nouns and less for noncount nouns. I'm asking because my word processor is asking me to change fewer to less in the ff context: Fewer than one percent of Spanish students around the world have mastered the subjunctive.

It is true that with percents, kilos, tonnes, litres and other words of measurement "less" is used, not "fewer". It is probably because the reference is made to the whole bulk rather than counting the units of measurement one by one.

I know that you use few for count nouns and less for noncount nouns. I'm asking because my word processor is asking me to change fewer to less in the ff context: Fewer than one percent of Spanish students around the world have mastered the subjunctive.

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Your sentence is fine grammatically, despite the nagging spell-checker, however note that "Spanish students" (like English students, etc.) can be either students of Spanish citizenship OR students of the Spanish language.

I would say something like "Fewer than one percent of Spanish-language students around the world have mastered the subjunctive."

Aw come on guys, you are discussing eccentric and unreal questions. It's no wonder you are quibbling over the answers. How many angels can dance on the point of a full stop? Is a the circular part of a comma bigger or smaller than a full stop. What is the standard aspect ratio of the vertical part of an exclamation mark.
The real world does not include asking the question "How many/much do/does 1% of the students come to?"

1) How many do 1% of the students come to? – How many (students) do one percent of the students come to?
2) How many does 1% of the students come to? - How many (students) does one percent of the students come to?
It seems to me that 2 is more logical.

But wouldn't it be better to rephrase it, by and large, into something like